Speaking during a visit to Israel to reassure the Washington ally over Mr Trump’s sudden decision to pull forces out of north-eastern Syria, Mr Bolton said there was no timetable for the exit.
“There are objectives that we want to accomplish that condition the withdrawal,” he told reporters in Jerusalem on Sunday, adding this included the defeat of Isis in Syria.
But Mr Bolton added that there was no unlimited commitment from the US on keeping troops in the region.
The remarks are the first public confirmation the withdrawal has been slowed, after Mr Trump faced widespread criticism over his sudden decision to pull 2,000 US service personnel from Syria.
His withdrawal plan drew the ire of many of the country’s close allies and led to the resignation of defence secretary Jim Mattis, who cited irreconcilable policy difference with the president.
Mr Trump’s move has raised fears over clearing the way for a Turkey assault on Kurdish fighters in Syria, who have fought alongside America troops against Isis forces.
Turkey considers the Syrian Kurdish People’s Protection Units, or YPG, a terrorist group linked to an insurgency within its own borders.
Mr Bolton, who is due to meet with Turkish president Recep Tayyip Erdogan in the coming days, said any withdrawal would rest on assurances of the safety of Kurdish people in the region.
He stated Mr Trump would “not allow Turkey to kill the Kurds”, adding: “That’s what the president said, the ones that fought with us”.
Mr Bolton said the US has asked its Kurdish allies to “stand fast now” and refrain from seeking protection from Russia or Syrian President Bashar al-Assad’s government.
“I think they know who their friends are,” he said, speaking of the Kurds.
He said chairman of the joint chiefs of staff General Joseph Dunford would continue negotiations with his Turkish counterparts this week to seek protection for America’s Kurdish allies in Syria.
Mr Bolton announced US troops would remain at the critical area of al-Tanf, in southern Syria, to counter growing Iranian activity in the region.
He defended the legal basis for the deployment, saying it was justified by the president’s constitutional authority, adding: “I’m a strong believer in Article II.”
Mr Bolton is to have dinner with Israel’s prime minister, Benjamin Netanyahu, on Sunday evening to discuss the pace of the US withdrawal, American troop levels in the region, and the US commitment to push back on Iranian regional expansionism.
He was expected to explain that some US troops based in Syria to fight Isis will shift to Iraq with the same mission and that the al-Tanf base would remain.
The US national security adviser toured the ancient tunnels beneath the Western Wall in Jerusalem‘s Old City on Sunday.
He watched a virtual reality tour of the historic site and dined there with his Israeli equivalent, as well as US Ambassador to Israel David Friedman and Israel‘s ambassador to the US, Ron Dermer.
Visiting American officials typically avoid holding official meetings in parts of east Jerusalem, which is contested between Israelis and Palestinians. Mr Trump himself, however, also toured the area in a previous visit.
Additional reporting by AP
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